Compact Representation of Uncertainty in Hierarchical Clustering

Hierarchical clustering is a fundamental task often used to discover meaningful structures in data, such as phylogenetic trees, taxonomies of concepts, subtypes of cancer, and cascades of particle decays in particle physics. When multiple hierarchical clusterings of the data are possible, it is useful to represent uncertainty in the clustering through various probabilistic quantities. Existing approaches represent uncertainty for a range of models; however, they only provide approximate inference. This paper presents dynamic-programming algorithms and proofs for exact inference in hierarchical clustering. We are able to compute the partition function, MAP hierarchical clustering, and marginal probabilities of sub-hierarchies and clusters. Our method supports a wide range of hierarchical models and only requires a cluster compatibility function. Rather than scaling with the number of hierarchical clusterings of $n$ elements ($\omega(n n! / 2^{n-1})$), our approach runs in time and space proportional to the significantly smaller powerset of $n$. Despite still being large, these algorithms enable exact inference in small-data applications and are also interesting from a theoretical perspective. We demonstrate the utility of our method and compare its performance with respect to existing approximate methods.